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Thursday, November 22, 2012

Breaking News: IDiots Don't Understand Genomes or Biology

Just when you think they couldn't get more stupid, along comes some IDiot to prove you wrong. Here's the latest from an anonymous contributor at Evolution News & Views [Your Genome? Which One?].

A new finding about DNA differences in somatic cells overthrows a common assumption and might have dramatic implications for evolutionary studies.

Young's Law (from Murphy's catalog of perverse tendencies in nature) states that all great discoveries are made by mistake. A corollary is that the greater the funding, the longer it takes to make the mistake, but we won't go there. Anyway, a team of Yale scientists wasn't looking to overturn a huge assumption in genetics -- but they did. The ripple effects of their discovery remain to be seen.

We've all been told that every cell in our body has a copy of our unique genetic code. That's one of those simplistic beliefs that sounds sensible but is almost impossible to check. Doesn't the whole body arise from cell divisions of a single zygote with its unique genetic code? Yes, but it doesn't necessarily follow that the genes in cells downstream don't get modified. That was just assumed....

"Somatic mosaicism" is jargon for the finding that genomes differ from cell to cell -- not only in copy number variations (CNV's), but in single nucleotide polymorphisms (SNP's). The assumption that you have one genome is thus falsified. You have lots of genomes!

Okay, let's take a poll.

How many of you thought that mutations such as nucleotide substitutions, deletions, and insertions, could never take place during the thousands of generations that give rise to our somatic cells? (How were they supposed to be suppressed?)

How many of you thought that all of our cells, including red blood cells, contain copies of our unmodified genome?

How many of you thought that there were no polyploid cells in our liver?

How many of you thought that B cells, and T cells (and others) contain the same identical copy of our genome that's found in germ cells?

How many of you thought that spermatocytes and ovaries have exactly the same genome as our original zygote?

How many of you thought that cancer-causing gene rearrangements and mutations in somatic cells were impossible?

How many of you are completely ignorant of any medical problems due to genetic mosaicism?

If you answered "yes" to all of those questions then, congratulations!, you're as smart as an IDiot.

Sheeesh!

One thing is clear at this stage: the assumption that each individual has a unique genome has been overthrown to some extent. Think how this might impact common evolutionary studies. For years, evolutionists have claimed small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? Remember, the Yale team found differences between cells in the same organ -- human skin. If the percent difference grows or shrinks depending on the source, any conclusions about human-chimp similarities would prove unreliable.

24 comments
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Just one question for this anonymous commenter (and I'll bet he's glad he chose to stay anonymous!): is this remarkable discovery you're alluding to something that was made in, like, the 1920s? Because I'm pretty sure we knew about karyotype variation in the 1920s.

I had learned about this research finding a few days ago, I think from Science News. I know that abundant copy number variations had been known to exist between individuals, and so it is not really surprising that they occur within an individual. Anyway, IDiots will be IDiotic. The differences between humans and chimps are not b/c of these sorts of differences, but are instead due to differences in exons and gene regulatory regions. Duh.

I just reviewed a paper where the authors kept saying "genetically identical mice" when they meant "mice from the same genetic background" or "from the same inbred strain". I pointed this out in two rounds of review, but the authors did not want to change it, and the editors did not take this point seriously. This error will probably be there in the upcoming Cell paper.

What if the percent difference is a function of the source cells used?

Since the difference would only increase from the zygotic stage on, wouldn't that mean that we have overestimated the human-chimp difference? And that our genomes are actually MORE similar? I would think that ID creationists would try to argue the other way.

The ID drivel shows that their crowd doesn't even understand how to appropriate the study for their own profit. A clear example of saying anything, just in case, and with no regard about how idiotic they make themselves look. Anyway, the critique is to the point, and if weren't for science's duty to fight ignorance, the ID post wouldn't deserve any attention. Anyway, the Yale study only adds to the understanding we already had on the topic. Perhaps even some more detail to the picture... which is always welcomed. The clowns, like Paul calls them, cannot even provide entertainment...

The funniest thing about the rational the IDiots extract from the paper is that it is usually them who claim that genomes can not change because this would require some intelligent intervention. Since they can not totally ignore mutations they usually sum them up as genetic entropy that would lead to the death of affected cells or organisms. In the current case they of course ignore the fact that albeit neighbouring cells contain different sequences the organism obviously is doing well because these facts can only be explained if junk DNA exists.

Good point, the alternative for them is to accept that all their imagined to be functional DNA of any organism can actually mutate to a substantial degree and still produce a viable organism, which seems to contradict when they insist there's only a few specific functional sequences in a gigantic desert of nonfunctionality.

"Think how this might impact common evolutionary studies. For years, evolutionists have claimed small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? "

I find it really cute how enthusiastically this was written. You can feel their excitement, thinking they're really onto something!

What if the percent difference is a function of the source cells used?

So do the work and demonstrate whether or not the apparent species distance varies with genetic distance from the zygote? Or look it up. Fame and fortune await if you can debunk relatedness that way.

ENV might also want to get onto the respective Genome Project people and tell them their genomes are really tissue type genomes - and probably just from individuals - and not representative of the species at fresh zygote level. They were probably wondering.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.